data_4LKK # _model_server_result.job_id JOF857PQvofzRNtAhJubSQ _model_server_result.datetime_utc '2024-12-01 09:42:53' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4lkk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 4LKK # _exptl.entry_id 4LKK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4LKK _cell.length_a 117.143 _cell.length_b 117.143 _cell.length_c 297.664 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LKK _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N ? 4 F N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 SIA _pdbx_entity_branch_link.comp_id_2 GAL _pdbx_entity_branch_link.atom_id_1 C2 _pdbx_entity_branch_link.leaving_atom_id_1 O2 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C GAL 1 C 1 GAL A 802 GAL 3 n C SIA 2 C 2 SIA A 801 SIA # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 2 A CYS 4 1_555 B SG CYS 136 B CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 40 A CYS 42 1_555 A SG CYS 266 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 52 A CYS 54 1_555 A SG CYS 64 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf4 A SG CYS 85 A CYS 87 1_555 A SG CYS 127 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf5 A SG CYS 270 A CYS 272 1_555 A SG CYS 294 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 B SG CYS 143 B CYS 465 1_555 B SG CYS 147 B CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 26 A ASN 28 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 229 A ASN 231 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 B ND2 ASN 81 B ASN 403 1_555 F C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 C O6 GAL . C GAL 1 1_555 C C2 SIA . C SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 NAG sing 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4LKK _atom_sites.fract_transf_matrix[1][1] 0.008537 _atom_sites.fract_transf_matrix[1][2] 0.004929 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009857 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.003359 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 NAG A 1 601 601 NAG NAG . E 4 NAG A 1 602 602 NAG NAG . F 4 NAG B 1 501 603 NAG NAG . G 5 HOH A 1 701 2 HOH HOH . G 5 HOH A 2 702 5 HOH HOH . G 5 HOH A 3 703 6 HOH HOH . G 5 HOH A 4 704 7 HOH HOH . G 5 HOH A 5 705 8 HOH HOH . G 5 HOH A 6 706 9 HOH HOH . G 5 HOH A 7 707 11 HOH HOH . G 5 HOH A 8 708 12 HOH HOH . G 5 HOH A 9 709 13 HOH HOH . G 5 HOH A 10 710 14 HOH HOH . G 5 HOH A 11 711 17 HOH HOH . G 5 HOH A 12 712 18 HOH HOH . G 5 HOH A 13 713 20 HOH HOH . G 5 HOH A 14 714 21 HOH HOH . G 5 HOH A 15 715 24 HOH HOH . G 5 HOH A 16 716 26 HOH HOH . G 5 HOH A 17 717 27 HOH HOH . G 5 HOH A 18 718 28 HOH HOH . G 5 HOH A 19 719 30 HOH HOH . G 5 HOH A 20 720 31 HOH HOH . G 5 HOH A 21 721 32 HOH HOH . G 5 HOH A 22 722 33 HOH HOH . G 5 HOH A 23 723 34 HOH HOH . G 5 HOH A 24 724 38 HOH HOH . G 5 HOH A 25 725 40 HOH HOH . G 5 HOH A 26 726 41 HOH HOH . G 5 HOH A 27 727 44 HOH HOH . G 5 HOH A 28 728 45 HOH HOH . G 5 HOH A 29 729 46 HOH HOH . G 5 HOH A 30 730 47 HOH HOH . G 5 HOH A 31 731 48 HOH HOH . G 5 HOH A 32 732 49 HOH HOH . G 5 HOH A 33 733 50 HOH HOH . G 5 HOH A 34 734 51 HOH HOH . G 5 HOH A 35 735 52 HOH HOH . G 5 HOH A 36 736 53 HOH HOH . G 5 HOH A 37 737 54 HOH HOH . G 5 HOH A 38 738 55 HOH HOH . G 5 HOH A 39 739 56 HOH HOH . G 5 HOH A 40 740 57 HOH HOH . G 5 HOH A 41 741 58 HOH HOH . G 5 HOH A 42 742 59 HOH HOH . G 5 HOH A 43 743 61 HOH HOH . G 5 HOH A 44 744 63 HOH HOH . G 5 HOH A 45 745 64 HOH HOH . G 5 HOH A 46 746 65 HOH HOH . G 5 HOH A 47 747 66 HOH HOH . G 5 HOH A 48 748 67 HOH HOH . G 5 HOH A 49 749 70 HOH HOH . G 5 HOH A 50 750 73 HOH HOH . G 5 HOH A 51 751 75 HOH HOH . G 5 HOH A 52 752 76 HOH HOH . G 5 HOH A 53 753 78 HOH HOH . G 5 HOH A 54 754 79 HOH HOH . G 5 HOH A 55 755 80 HOH HOH . G 5 HOH A 56 756 83 HOH HOH . G 5 HOH A 57 757 84 HOH HOH . G 5 HOH A 58 758 85 HOH HOH . G 5 HOH A 59 759 86 HOH HOH . G 5 HOH A 60 760 88 HOH HOH . G 5 HOH A 61 761 89 HOH HOH . G 5 HOH A 62 762 90 HOH HOH . G 5 HOH A 63 763 91 HOH HOH . G 5 HOH A 64 764 92 HOH HOH . G 5 HOH A 65 765 94 HOH HOH . G 5 HOH A 66 766 95 HOH HOH . G 5 HOH A 67 767 97 HOH HOH . G 5 HOH A 68 768 99 HOH HOH . G 5 HOH A 69 769 101 HOH HOH . G 5 HOH A 70 770 103 HOH HOH . G 5 HOH A 71 771 105 HOH HOH . G 5 HOH A 72 772 106 HOH HOH . G 5 HOH A 73 773 107 HOH HOH . G 5 HOH A 74 774 109 HOH HOH . G 5 HOH A 75 775 110 HOH HOH . G 5 HOH A 76 776 111 HOH HOH . G 5 HOH A 77 777 112 HOH HOH . G 5 HOH A 78 778 114 HOH HOH . H 5 HOH B 1 601 1 HOH HOH . H 5 HOH B 2 602 3 HOH HOH . H 5 HOH B 3 603 4 HOH HOH . H 5 HOH B 4 604 10 HOH HOH . H 5 HOH B 5 605 15 HOH HOH . H 5 HOH B 6 606 16 HOH HOH . H 5 HOH B 7 607 19 HOH HOH . H 5 HOH B 8 608 22 HOH HOH . H 5 HOH B 9 609 23 HOH HOH . H 5 HOH B 10 610 25 HOH HOH . H 5 HOH B 11 611 29 HOH HOH . H 5 HOH B 12 612 35 HOH HOH . H 5 HOH B 13 613 36 HOH HOH . H 5 HOH B 14 614 37 HOH HOH . H 5 HOH B 15 615 39 HOH HOH . H 5 HOH B 16 616 43 HOH HOH . H 5 HOH B 17 617 60 HOH HOH . H 5 HOH B 18 618 62 HOH HOH . H 5 HOH B 19 619 68 HOH HOH . H 5 HOH B 20 620 69 HOH HOH . H 5 HOH B 21 621 71 HOH HOH . H 5 HOH B 22 622 72 HOH HOH . H 5 HOH B 23 623 74 HOH HOH . H 5 HOH B 24 624 77 HOH HOH . H 5 HOH B 25 625 81 HOH HOH . H 5 HOH B 26 626 82 HOH HOH . H 5 HOH B 27 627 87 HOH HOH . H 5 HOH B 28 628 93 HOH HOH . H 5 HOH B 29 629 96 HOH HOH . H 5 HOH B 30 630 98 HOH HOH . H 5 HOH B 31 631 100 HOH HOH . H 5 HOH B 32 632 102 HOH HOH . H 5 HOH B 33 633 104 HOH HOH . H 5 HOH B 34 634 108 HOH HOH . H 5 HOH B 35 635 113 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 NAG . . . F 4 -9.464 -8.628 46.882 1 80.7 ? C1 NAG 501 B 1 HETATM 2 C C2 NAG . . . F 4 -9.642 -9.599 45.71 1 84.98 ? C2 NAG 501 B 1 HETATM 3 C C3 NAG . . . F 4 -11.094 -10.03 45.528 1 87.81 ? C3 NAG 501 B 1 HETATM 4 C C4 NAG . . . F 4 -11.765 -10.363 46.856 1 87.49 ? C4 NAG 501 B 1 HETATM 5 C C5 NAG . . . F 4 -11.551 -9.229 47.855 1 86.45 ? C5 NAG 501 B 1 HETATM 6 C C6 NAG . . . F 4 -12.205 -9.506 49.206 1 86.13 ? C6 NAG 501 B 1 HETATM 7 C C7 NAG . . . F 4 -8.42 -9.617 43.577 1 82.91 ? C7 NAG 501 B 1 HETATM 8 C C8 NAG . . . F 4 -7.924 -8.8 42.415 1 78.11 ? C8 NAG 501 B 1 HETATM 9 N N2 NAG . . . F 4 -9.166 -8.98 44.48 1 84.86 ? N2 NAG 501 B 1 HETATM 10 O O3 NAG . . . F 4 -11.131 -11.145 44.665 1 89.28 ? O3 NAG 501 B 1 HETATM 11 O O4 NAG . . . F 4 -13.142 -10.581 46.641 1 89.45 ? O4 NAG 501 B 1 HETATM 12 O O5 NAG . . . F 4 -10.165 -9.032 48.044 1 84.99 ? O5 NAG 501 B 1 HETATM 13 O O6 NAG . . . F 4 -11.931 -8.446 50.097 1 86.3 ? O6 NAG 501 B 1 HETATM 14 O O7 NAG . . . F 4 -8.146 -10.813 43.666 1 82.14 ? O7 NAG 501 B 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #